I do this often, I start reaper, record some stuff, then think: "i'm gonna save this in a directory".
I then go and make the directory, say: s:\music stuff\project123
Then, when I save the project in the dialog box, I tell reaper to 'Move all associated files to project directory" (there's a checkbox at the bottom of the dialog box). This puts everything in my newly created project123 directory.
Sorry for the loss, I've gotten some projects all over like this as well. After a few years, I've gotten in this habit above, and it's worked well.
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